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552 lines
16 KiB
C++
552 lines
16 KiB
C++
//
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// Copyright (C) 2015 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/utils.h>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/Depictor/RDDepictor.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/MolDraw2D/MolDraw2D.h>
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#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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using namespace RDKit;
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void test1(){
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std::cout << " ----------------- Test 1" << std::endl;
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{
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std::string smiles="CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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std::ofstream outs("test1_1.svg");
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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outs.flush();
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delete m;
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}
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{
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// make sure this works with the stringstream too:
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std::string smiles="CO[C@@H](O)C1=C(O[C@H](F)Cl)C=C1ONNC[NH3+]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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MolDraw2DSVG drawer(300,300);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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std::string text = drawer.getDrawingText();
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TEST_ASSERT(text.find("<svg:svg")!=std::string::npos);
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TEST_ASSERT(text.find("</svg:svg>")!=std::string::npos);
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delete m;
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}
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{
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std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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std::ofstream outs("test1_2.svg");
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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outs.flush();
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delete m;
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}
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{
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std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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std::ofstream outs("test1_3.svg");
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MolDraw2DSVG drawer(300,300,outs);
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std::vector<int> highlights;
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highlights.push_back(0);
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highlights.push_back(4);
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highlights.push_back(5);
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drawer.drawMolecule(*m,&highlights);
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drawer.finishDrawing();
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outs.flush();
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delete m;
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}
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std::cout << " Done" << std::endl;
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}
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#ifdef RDK_CAIRO_BUILD
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#include <cairo.h>
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#include "MolDraw2DCairo.h"
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void test2(){
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std::cout << " ----------------- Test 2" << std::endl;
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{
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std::string smiles="CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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MolDraw2DCairo drawer(300,300);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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drawer.writeDrawingText("test2_1.png");
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delete m;
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}
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{
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std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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MolDraw2DCairo drawer(300,300);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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std::string drawing=drawer.getDrawingText();
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std::ofstream ofs("test2_2.png");
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ofs.write(drawing.c_str(),drawing.size());
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delete m;
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}
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{
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// ensure we still work with a client-provided drawing context
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std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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cairo_surface_t *surface =
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cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
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cairo_t *cr = cairo_create (surface);
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MolDraw2DCairo drawer(300,300,cr);
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std::vector<int> highlights;
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highlights.push_back(0);
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highlights.push_back(4);
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highlights.push_back(5);
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drawer.drawMolecule(*m,&highlights);
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drawer.finishDrawing();
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cairo_destroy (cr);
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cairo_surface_write_to_png (surface, "test2_3.png");
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cairo_surface_destroy (surface);
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delete m;
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}
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std::cout << " Done" << std::endl;
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}
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#else // RDK_CAIRO_BUILD
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void test2(){
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}
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#endif
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void test3(){
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std::cout << " ----------------- Test 3" << std::endl;
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{
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std::string smiles="C1CC1CC1ON1";
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std::string nameBase="test3_1";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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static const int ha[] = {0,3,4,5};
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std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
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std::map<int,std::string> atomLabels;
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atomLabels[2]="C1";
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atomLabels[1]="a<sub>3</sub><sup>4</sup>";
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atomLabels[0]="[CH2;X2:4]";
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atomLabels[6]="[NH2+:7]";
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions().atomLabels = atomLabels;
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drawer.drawMolecule(*m,&highlight_atoms);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions().atomLabels = atomLabels;
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drawer.drawMolecule(*m,&highlight_atoms);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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{
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std::string smiles="C1CC1CC1ON1";
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std::string nameBase="test3_2";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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static const int ha[] = {0,3,4,5};
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std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions().circleAtoms=false;
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drawer.drawMolecule(*m,&highlight_atoms);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions().circleAtoms=false;
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drawer.drawMolecule(*m,&highlight_atoms);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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{
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std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
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std::string nameBase="test3_3";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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static const int ha[] = {11,12,13,14,15,16};
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std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
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std::map<int,DrawColour> highlight_colors;
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highlight_colors[12]=DrawColour(0,0,1);
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highlight_colors[13]=DrawColour(0,1,0);
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions().circleAtoms=true;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions().circleAtoms=true;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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{
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std::string smiles="Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
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std::string nameBase="test3_4";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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static const int ha[] = {11,12,13,14,15,16,3};
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std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
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std::map<int,DrawColour> highlight_colors;
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highlight_colors[12]=DrawColour(.5,.5,1);
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highlight_colors[13]=DrawColour(.5,1,.5);
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MolDrawOptions options;
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options.circleAtoms=true;
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options.highlightColour=DrawColour(1,.5,.5);
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options.continuousHighlight=true;
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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{
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std::string smiles="CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
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std::string nameBase="test3_5";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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static const int ha[] = {17,18,19,20,21,6,7,8,9,31,32};
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std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
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std::map<int,DrawColour> highlight_colors;
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MolDrawOptions options;
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options.circleAtoms=true;
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options.highlightColour=DrawColour(1,.5,.5);
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options.continuousHighlight=true;
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(200,200);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(200,200,outs);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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{
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std::string smiles="CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
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std::string nameBase="test3_6";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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MolDrawOptions options;
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static const int ha1[] = {17,18,19,20,21};
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std::vector<int> highlight_atoms1(ha1, ha1+sizeof(ha1)/sizeof(int));
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options.atomRegions.push_back(highlight_atoms1);
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static const int ha2[] = {6,7,8,9,31,32};
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std::vector<int> highlight_atoms2(ha2, ha2+sizeof(ha2)/sizeof(int));
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options.atomRegions.push_back(highlight_atoms2);
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options.includeAtomTags=true;
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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{
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std::string smiles="CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
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std::string nameBase="test3_7";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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MolDrawOptions options;
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options.continuousHighlight=true;
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static const int ha[] = {17,20,25};
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std::vector<int> highlight_atoms(ha, ha+sizeof(ha)/sizeof(int));
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std::map<int,double> highlight_radii;
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highlight_radii[17]=0.5;
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highlight_radii[20]=1.0;
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std::map<int,DrawColour> highlight_colors;
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highlight_colors[17]=DrawColour(.5,.5,1.);
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors,&highlight_radii);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m,&highlight_atoms,&highlight_colors,&highlight_radii);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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std::cout << " Done" << std::endl;
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}
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void test4(){
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std::cout << " ----------------- Test 4" << std::endl;
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{
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std::string fName = getenv("RDBASE");
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fName += "/Code/GraphMol/MolDraw2D/test_dir";
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fName += "/clash.mol";
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ROMol *m = MolFileToMol(fName);
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std::string nameBase="test4_1";
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TEST_ASSERT(m);
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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outs.flush();
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}
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delete m;
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}
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std::cout << " Done" << std::endl;
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}
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void test5(){
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std::cout << " ----------------- Test 5" << std::endl;
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{
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std::string smiles="*c1cc(*)cc(*)c1";
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std::string nameBase="test5_1";
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ROMol *m = SmilesToMol(smiles);
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TEST_ASSERT(m);
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RDDepict::compute2DCoords(*m);
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WedgeMolBonds(*m,&(m->getConformer()));
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MolDrawOptions options;
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options.dummiesAreAttachments=true;
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options.atomLabels[0]="R1";
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#ifdef RDK_CAIRO_BUILD
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{
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MolDraw2DCairo drawer(300,300);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
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drawer.writeDrawingText(nameBase+".png");
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}
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#endif
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{
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std::ofstream outs((nameBase+".svg").c_str());
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MolDraw2DSVG drawer(300,300,outs);
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drawer.drawOptions() = options;
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drawer.drawMolecule(*m);
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drawer.finishDrawing();
|
|
outs.flush();
|
|
}
|
|
delete m;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
|
|
|
|
#ifdef RDK_TEST_MULTITHREADED
|
|
#include <boost/thread.hpp>
|
|
namespace {
|
|
void runblock(const std::vector<ROMol *> &mols,const std::vector<std::string> &refData,
|
|
unsigned int count,unsigned int idx){
|
|
for(unsigned int j=0;j<200;j++){
|
|
for(unsigned int i=0;i<mols.size();++i){
|
|
if(i%count != idx) continue;
|
|
ROMol *mol = mols[i];
|
|
MolDraw2DSVG drawer(300,300);
|
|
drawer.drawMolecule(*mol);
|
|
drawer.finishDrawing();
|
|
std::string text = drawer.getDrawingText();
|
|
TEST_ASSERT(text==refData[i]);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
void testMultiThreaded(){
|
|
std::cout << " ----------------- Test multi-threaded drawing" << std::endl;
|
|
std::string fName = getenv("RDBASE");
|
|
fName += "/Data/NCI/first_200.props.sdf";
|
|
RDKit::SDMolSupplier suppl(fName);
|
|
std::cerr<<"reading molecules"<<std::endl;
|
|
std::vector<ROMol *> mols;
|
|
while(!suppl.atEnd()&&mols.size()<100){
|
|
ROMol *mol=0;
|
|
try{
|
|
mol=suppl.next();
|
|
} catch(...){
|
|
continue;
|
|
}
|
|
if(!mol) continue;
|
|
mols.push_back(mol);
|
|
}
|
|
|
|
std::cerr<<"generating reference drawings"<<std::endl;
|
|
std::vector<std::string> refData(mols.size());
|
|
for(unsigned int i=0;i<mols.size();++i){
|
|
MolDraw2DSVG drawer(300,300);
|
|
drawer.drawMolecule(*(mols[i]));
|
|
drawer.finishDrawing();
|
|
refData[i]=drawer.getDrawingText();
|
|
TEST_ASSERT(refData[i].find("<svg:svg")!=std::string::npos);
|
|
TEST_ASSERT(refData[i].find("</svg:svg>")!=std::string::npos);
|
|
}
|
|
|
|
boost::thread_group tg;
|
|
unsigned int count=4;
|
|
std::cerr<<"processing"<<std::endl;
|
|
for(unsigned int i=0;i<count;++i){
|
|
std::cerr<<" launch :"<<i<<std::endl;std::cerr.flush();
|
|
tg.add_thread(new boost::thread(runblock,mols,refData,count,i));
|
|
}
|
|
tg.join_all();
|
|
std::cerr<<" Done"<<std::endl;
|
|
}
|
|
#else
|
|
void testMultiThreaded(){
|
|
}
|
|
#endif
|
|
|
|
int main(){
|
|
RDLog::InitLogs();
|
|
test1();
|
|
test2();
|
|
test3();
|
|
test4();
|
|
test5();
|
|
testMultiThreaded();
|
|
}
|